For most of the game, Yakra XIII disguises himself as King Guardia XXXIII's Chancellor. He hired Fiends as to impersonate Royal Guards for the Prison Towers and constructs the Dragon Tank. After Crono and his friends return to the present, Yakra XIII states that Crono had kidnapped Marle and puts him on trial in the castle's courtroom. Crono is charged with the abduction of Princess Nadia. People are brought in from Leene Square who interacted with Crono and Marle as well as people hired by the Yakra XIII to falsely testify against Crono. When Crono is taken to the Prison Towers, even if he has been pronounced innocent, Yakra XIII tells the ward that he has been found guilty and will be executed in three days.

Yakra XIII sends the Dragon Tank to kill Crono when he escapes, but he defeats it with he help of Lucca. The Fiend then chases them into Guardia Forest intending to execute the death sentence himself. However, they escape through a Gate.

Later, when Marle enters the castle, he revealed the death of her mother, Queen Aliza, as being the result of her father's negligence. She desperately asked to see King Guardia XXXIII one last time, but the Chancellor refused to grant audience, saying that the King could not leave his work unattended.

Eventually, the King is put on trial. Yakra XIII prosecutes the King for allegedly selling the royal heirloom, the Rainbow Shell, when a falsified ancestral will proclaims the shell should have been unveiled at the Moonlight Parade. Marle enters the courtroom, and the King tells her that he is being framed by the Chancellor. The Chancellor asks for proof, saying that if the King has not sold the heirloom, then it should be somewhere in the castle. Shortly after, Marle is kicked out of the courtroom. Marle and two others decide to search the castle for the Rainbow Shell. Meanwhile, the King's trial continues, and as the real Chancellor did in the beginning of the game, the false Chancellor brings forward people to falsely testify against the King. The party finds the Rainbow Shell in the castle, and breaks into the courtroom by jumping through the stained-glass mural behind the Judge's seat.

The Chancellor says they are too late; a guilty verdict had been reached. At this time, she reveals a shard of the Rainbow Shell, at which point the Chancellor reveals he is really Yakra XIII. Inflamed with rage at this ancestor, Yakra's humiliation for failing to capture Queen Leene, he attacks the party.
After he is defeated, he drops a key that opens the box which the real Chancellor is locked in.